#' @title Creating a bigwig using RSEM
#' @description This function executes the docker container rsemstar where RSEM is installed and create a bigwig file for genomic data visualization
#'
#' @param group, a character string. Two options: \code{"sudo"} or \code{"docker"}, depending to which group the user belongs
#' @param bam.folder, a character string indicating where BAM SORTED file is located
#' @param scratch.folder, a character string indicating the scratch folder where docker container will be mounted
#'
#' @return output.bw, which is the bigwig
#' @examples
#'\dontrun{
#' #downloading fastq files
#' rsemBw(group="docker",bam.folder=getwd(), scratch.folder="/data/scratch")
#'
#'
#' }
#' @export
rsemBw <- function(group=c("sudo","docker"),bam.folder=getwd(), scratch.folder="/data/scratch"){
#running time 1
ptm <- proc.time()
#running time 1
home <- getwd()
setwd(bam.folder)
#initialize status
system("echo 0 > ExitStatusFile 2>&1")
test <- dockerTest()
if(!test){
cat("\nERROR: Docker seems not to be installed in your system\n")
system("echo 10 > ExitStatusFile 2>&1")
setwd(home)
return(10)
}
#########check scratch folder exist###########
if (!file.exists(scratch.folder)){
cat(paste("\nIt seems that the ",scratch.folder, "folder does not exist\n"))
system("echo 3 > ExitStatusFile 2>&1")
setwd(home)
return(3)
}
#############################################
tmp.folder <- gsub(":","-",gsub(" ","-",date()))
scrat_tmp.folder=file.path(scratch.folder, tmp.folder)
writeLines(scrat_tmp.folder,paste(bam.folder,"/tempFolderID", sep=""))
cat("\ncreating a folder in scratch folder\n")
dir.create(file.path(scratch.folder, tmp.folder))
dir.create(file.path(scratch.folder, tmp.folder,"/tmp"))
dir <- dir(path=bam.folder)
dir.info <- dir[which(dir=="run.info")]
if(length(dir.info)>0){
system(paste("chmod 777 -R", file.path(scratch.folder, tmp.folder)))
system(paste("cp ",bam.folder,"/run.info ", scratch.folder,"/",tmp.folder,"/run.info", sep=""))
}
dir <- dir[grep(".bam", dir)]
dir <- dir[which(dir=="Aligned.out.bam")]
cat("\ncopying \n")
if(length(dir)==0){
cat(paste("It seems that in ", bam.folder, "there is not a bam file"))
return(1)
}else{
system(paste("chmod 777 -R", file.path(scratch.folder, tmp.folder)))
system(paste("cp ",bam.folder,"/",dir, " ",scratch.folder,"/",tmp.folder,"/",dir, sep=""))
system(paste("chmod 777 -R", file.path(scratch.folder, tmp.folder)))
}
docker_fastq.folder=file.path("/data/scratch", tmp.folder)
params <- paste("--cidfile ",bam.folder,"/dockerID -v ",scratch.folder,":/data/scratch -d docker.io/rcaloger/rsemstar.2017.01 sh /bin/rsem_bw.sh ",docker_fastq.folder," ", dir," ",bam.folder, sep="")
resultRun=runDocker(group="sudo", params=params)
#waiting for the end of the container work
if(resultRun==0){
cat("\n bigwig using RSEM is finished\n")
}
#system(paste("chmod 777 -R", file.path(scratch.folder, tmp.folder)))
con <- file(paste(file.path(scratch.folder, tmp.folder),"out.info", sep="/"), "r")
tmp <- readLines(con)
close(con)
for(i in tmp){
i <- sub("mv ",paste("mv ",file.path(scratch.folder, tmp.folder),"/",sep=""),i)
system(i)
}
#running time 2
ptm <- proc.time() - ptm
con <- file(paste(bam.folder,"run.info", sep="/"), "r")
tmp.run <- readLines(con)
close(con)
tmp.run[length(tmp.run)+1] <- paste("user run time mins ",ptm[1]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("system run time mins ",ptm[2]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("elapsed run time mins ",ptm[3]/60, sep="")
writeLines(tmp.run,paste(bam.folder,"run.info", sep="/"))
#saving log and removing docker container
container.id <- readLines(paste(bam.folder,"/dockerID", sep=""), warn = FALSE)
system(paste("docker logs ", container.id, " >& ", substr(container.id,1,12),".log", sep=""))
system(paste("docker rm ", container.id, sep=""))
#removing temporary folder
cat("\n\nRemoving the rsem temporary file ....\n")
# system(paste("rm -R ",scrat_tmp.folder))
# system(paste("rm -f ",bam.folder,"/dockerID", sep=""))
# system(paste("rm -f ",bam.folder,"/tempFolderID", sep=""))
setwd(home)
}
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